
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:49 02/24/2011

Input data from file "/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7410.phylip" (19 taxa, 1034 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYI


Note: number of parameters compared to sample size
is low (Nchar/Nparams < 40). Consider the use of AICc.


(Output sorted by AICc. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AICc		wAICc	cwAICc
GTRIG	45	-2746.4216	5587.0335	0.8039	0.8039
GTRG	44	-2749.5687	5591.1415	0.1031	0.9070
GTRI	44	-2749.6750	5591.3540	0.0927	0.9997
HKYIG	41	-2758.7662	5603.0042	0.0003	0.9999
HKYI	40	-2762.0999	5607.5029	0.0000	1.0000
HKYG	40	-2762.2058	5607.7147	0.0000	1.0000
SYMIG	42	-2788.7775	5665.1999	0.0000	1.0000
K2PIG	38	-2793.8249	5666.6287	0.0000	1.0000
SYMG	41	-2792.0972	5669.6661	0.0000	1.0000
SYMI	41	-2792.3360	5670.1437	0.0000	1.0000
K2PI	37	-2797.1490	5671.1213	0.0000	1.0000
K2PG	37	-2797.2146	5671.2525	0.0000	1.0000
F81IG	40	-2810.7174	5704.7379	0.0000	1.0000
F81G	39	-2813.6497	5708.4382	0.0000	1.0000
F81I	39	-2813.8395	5708.8179	0.0000	1.0000
JC69IG	37	-2838.9634	5754.7501	0.0000	1.0000
JC69G	36	-2841.4439	5757.5597	0.0000	1.0000
JC69I	36	-2841.8593	5758.3907	0.0000	1.0000
GTR	43	-2842.0818	5773.9858	0.0000	1.0000
HKY	39	-2850.6080	5782.3548	0.0000	1.0000
K2P	36	-2883.1776	5841.0272	0.0000	1.0000
SYM	40	-2879.1244	5841.5518	0.0000	1.0000
F81	38	-2894.9862	5868.9513	0.0000	1.0000
JC69	35	-2922.4118	5917.3486	0.0000	1.0000



(Output sorted by AIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2746.4216	5582.8433	0.8182	0.8182
GTRG	44	-2749.5687	5587.1375	0.0956	0.9138
GTRI	44	-2749.6750	5587.3500	0.0860	0.9998
HKYIG	41	-2758.7662	5599.5324	0.0002	1.0000
HKYI	40	-2762.0999	5604.1998	0.0000	1.0000
HKYG	40	-2762.2058	5604.4116	0.0000	1.0000
SYMIG	42	-2788.7775	5661.5551	0.0000	1.0000
K2PIG	38	-2793.8249	5663.6498	0.0000	1.0000
SYMG	41	-2792.0972	5666.1944	0.0000	1.0000
SYMI	41	-2792.3360	5666.6719	0.0000	1.0000
K2PI	37	-2797.1490	5668.2980	0.0000	1.0000
K2PG	37	-2797.2146	5668.4292	0.0000	1.0000
F81IG	40	-2810.7174	5701.4348	0.0000	1.0000
F81G	39	-2813.6497	5705.2993	0.0000	1.0000
F81I	39	-2813.8395	5705.6790	0.0000	1.0000
JC69IG	37	-2838.9634	5751.9268	0.0000	1.0000
JC69G	36	-2841.4439	5754.8877	0.0000	1.0000
JC69I	36	-2841.8593	5755.7187	0.0000	1.0000
GTR	43	-2842.0818	5770.1636	0.0000	1.0000
HKY	39	-2850.6080	5779.2160	0.0000	1.0000
SYM	40	-2879.1244	5838.2487	0.0000	1.0000
K2P	36	-2883.1776	5838.3552	0.0000	1.0000
F81	38	-2894.9862	5865.9724	0.0000	1.0000
JC69	35	-2922.4118	5914.8235	0.0000	1.0000



(Output sorted by BIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-2762.0999	5801.8474	0.2898	0.2898
HKYG	40	-2762.2058	5802.0592	0.2607	0.5505
HKYIG	41	-2758.7662	5802.1212	0.2527	0.8032
GTRG	44	-2749.5687	5804.5498	0.0750	0.8782
GTRI	44	-2749.6750	5804.7623	0.0675	0.9457
GTRIG	45	-2746.4216	5805.1968	0.0543	1.0000
K2PI	37	-2797.1490	5851.1220	0.0000	1.0000
K2PG	37	-2797.2146	5851.2533	0.0000	1.0000
K2PIG	38	-2793.8249	5851.4150	0.0000	1.0000
SYMG	41	-2792.0972	5868.7832	0.0000	1.0000
SYMIG	42	-2788.7775	5869.0851	0.0000	1.0000
SYMI	41	-2792.3360	5869.2607	0.0000	1.0000
F81G	39	-2813.6497	5898.0058	0.0000	1.0000
F81I	39	-2813.8395	5898.3854	0.0000	1.0000
F81IG	40	-2810.7174	5899.0824	0.0000	1.0000
JC69G	36	-2841.4439	5932.7705	0.0000	1.0000
JC69I	36	-2841.8593	5933.6015	0.0000	1.0000
JC69IG	37	-2838.9634	5934.7508	0.0000	1.0000
HKY	39	-2850.6080	5971.9224	0.0000	1.0000
GTR	43	-2842.0818	5982.6348	0.0000	1.0000
K2P	36	-2883.1776	6016.2381	0.0000	1.0000
SYM	40	-2879.1244	6035.8963	0.0000	1.0000
F81	38	-2894.9862	6053.7376	0.0000	1.0000
JC69	35	-2922.4118	6087.7652	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7410.phylip = 1 - 1034;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7410.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7410.phylip = 1 - 1034;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7410.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7410.phylip = 1 - 1034;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7410.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

